2023/11/10 by Davide Gurnari, Aldo Guzmán-Sáenz, Gurnari, Davide +9 · 1 citation
Biochemistry, Genetics and Molecular Biology · Computer Science · #Bioinformatics and Genomic Networks #FOS: Biological sciences #Genomics (q-bio.GN) #Metabolomics and Mass Spectrometry Studies #Topological and Geometric Data Analysis
paper · pdf · doi:10.48550/arxiv.2311.06357
openalex publication_date 2023/11/10 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Identifying molecular signatures from complex disease patients with underlying symptomatic similarities is a significant challenge in the analysis of high dimensional multi-omics data. Topological data analysis (TDA) provides a way of extracting such information from the geometric structure of the data and identifying multiway higher-order relationships. Here, we propose an application of Harmonic persistent homology, which overcomes the limitations of ambiguous assignment of the topological information to the original elements in a representative topological cycle from the data. When applied to multi-omics data, this leads to the discovery of hidden patterns highlighting the relationships between different omic profiles, while allowing for common tasks in multi-omics analyses, such as disease subtyping, and most importantly biomarker identification for similar latent biological pathways that are associated with complex diseases. Our experiments on multiple cancer data show that harmonic persistent homology effectively dissects multi-omics data to identify biomarkers by detecting representative cycles predictive of disease subtypes.